According to Japan's public broadcaster NHK, another 10 people remain missing.
As the superstorm quickly approached land, the U.S. Geological Survey recorded a 5.3 magnitude earthquake centered off the coast of Tokyo.
To the north, a tornado tore through the city of Chiba, which saw power outages and damaged homes in a typhoon last month.
Hagibis -- which translates to "speed" in Filipino -- was forecast to be the country's worst typhoon in six decades. Maximum sustained winds were measured at up to 90 miles per hour, according to The Japan Meteorological Agency.
A representative for the agency warned citizens to "take all measures necessary to save your life."
"Be ready for rainfall of the kind that you have never experienced." official Yasushi Kajihara cautioned.
Kajihara also said that people who live near rivers -- several of which had flooded by late Saturday -- should seek refuge on the second floor or higher of any sturdy buildings if they were unable to evacuate in time.
Authorities also warned of mudslides, common in mountainous regions.
More than 170,000 people have evacuated and more than 390,000 homes suffered power outages.
Prime Minister Shinzo Abe called up 17,000 police and military troops for rescue operations at a disaster management meeting on Friday.
"The typhoon could cause power outages, damage to infrastructure, and significantly affect people's lives," he said.
Events including the Rugby World Cup matches and concerts were canceled along with air and ground transportation.
The last devastating typhoon struck Tokyo in 1958, killing more than 1,200 people and flooding half a million homes. Evacuation centers were set up in coastal towns, and people laid in wait on gymnasium floors.
Fox News' Travis Fedschun and the Associated Press contributed to this report.